{ "dataset": { "archive": "dandi", "id": "000005", "label": "DANDI:000005" }, "page": "datasets/dandi/000005/", "generated": "2026-10-22T21:23:47+00:00", "caution": "A failure to reproduce is not a finding that the paper is wrong. It may be a failure of the attempt.", "outcome_counts": { "reproduced": 5, "partially_reproduced": 9, "not_reproduced": 6, "blocked": 13 }, "outcome_counts_with_outside_data": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_elsewhere": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_links": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "attempts": [ { "id": "000005-yu-2016-02", "dataset": { "archive": "dandi", "id": "000005", "version": "0.220126.1853", "doi": "10.48324/dandi.000005/0.220126.1853" }, "key": "dandi:000005", "label": "DANDI:000005", "dataset_version": "0.220126.1853", "paper": "10.1038/nn.4412", "paper_title": "Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation", "date": "2026-10-20", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-10" }, "runner": null, "tier": "agent_verified", "deprecated": "", "deprecated_on": null, "entry": "000005-yu-2016", "entry_title": "VPM and layer 4 responses to touch and whisking, and their control by thalamus and FS interneurons (Yu et al. 2016)", "description": "Tests the claims written from the full text of Yu, Gutnisky, Hires and Svoboda (2016) on dandiset 000005, which holds silicon probe recordings in VPM and single-cell recordings in layer 4 of barrel cortex of mice locating a pole with their whiskers. It measures touch responses, whisking rates and phase coupling of VPM units, FS interneurons and excitatory cells, their membrane potential, and the effects of thalamic photoinhibition and of PV interneuron suppression, by the paper's methods as the claims file gives them.", "notebooks": [ { "path": "reproduce_yu_2016.ipynb", "title": "Reproducing Yu et al. (2016) from dandiset 000005", "executed": "notebooks/000005-yu-2016/reproduce_yu_2016.html" } ], "outcomes": [ { "claim": "behavior-touches", "statement": "Mice touched the pole often when it was within reach (lick trials, 5.7 +- 5.3 touches per trial over 4,147 trials) and rarely when it was distal (0.9 +- 3.4 over 4,173 trials); performance was 0.72 +- 0.11 in cortical and 0.71 +- 0.07 in VPM recordings.", "source": "Online Methods, Behavior, paragraph 2", "quote": "Mice touched the pole at a proximal location multiple times (number of touches ... Mice touched the pole at a distal location less often (number of touches, 0.9 \u00b1 3.4, mean \u00b1 s.d., 4,173 trials) and withheld licking. Average performance (proportion of correct trials) was 0.72 \u00b1 0.11 (mean \u00b1 s.d., during the recordings of 111 cells) for cortical recordings and 0.71 \u00b1 0.07 for VPM recordings (during the recordings of 29 cells).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "Under light reading (x), every trial, with all sessions (b) and principal-whisker touches (i), mice touch the pole 6.04 times per lick trial (9,794 trials) and 0.85 times per no-lick trial (8,223 trials), both within tolerance; no other reading puts both counts within tolerance. Under light reading (y), trials without light only, the same recordings give 5.74 and 0.80 (8,219 and 6,713 trials), and the no-lick count is outside tolerance. The matching trial counts are more than twice the paper's 4,147 and 4,173, and no reading gives the paper's counts (the nearest, 5,212 and 5,149, come from reading a with every trial). Performance averages 0.681 under (x) and 0.694 under (y) over all 122 cortical cells, within tolerance (0.703 and 0.718 without the flagged mice, a variant that no longer decides), and 0.585 over the 29 VPM units under both (the VPM sessions have no light), outside 0.71 +- 0.071. New claim.", "deviations": [ "The 111 control cortical cells of reading (a) cannot be identified, as the files do not mark the ION-cut mice; every cortical cell counts, as in every other group, and leaving out the cells of the 4 flagged mice is a variant." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "vpm-touch", "statement": "VPM neurons respond to active touch with a sharp, short-latency increase in spike rate (0.6 +- 0.5 spikes per touch, median 0.4; latency 3.2 +- 1.0 ms, median 2.5 ms).", "source": "Results, Chronic extracellular recordings from somatosensory thalamus, paragraph 1; Figure 1b,d; Figure 5b,c", "quote": "Neurons responded to active touch during behavior with an increase in spike rate (Fig. 1b). The peristimulus time ... histogram aligned to touch onset showed a sharp peak in spike rate (mean \u00b1 s.d., 0.6 \u00b1 0.5 spikes per touch; median, 0.4 spikes per touch), with short latency after touch onset (mean \u00b1 s.d., 3.2 \u00b1 1.0 ms; median, 2.5 ms)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "Over the 29 VPM units, spikes per touch (0 to 25 ms after minus 0 to 25 ms before onset, principal-whisker touches with ITI of at least 25 ms) average 0.403, median 0.268, outside 0.6 +- 0.093 and 0.4 +- 0.04. 25 units pass the latency exclusion; the latency has mean 5.64 ms and median 2.0 ms with the bin's left edge (O9 a) and 6.14 and 2.5 ms with its centre (O9 b), one unit at 71.5 ms. What the answer changed. The answer of 2026-10-20 says the paper does not fix the bin position, and the criterion now runs both; this attempt already showed both, the spikes per touch fail under either, and the outcome is unchanged. The measured latencies are those of O9 b, the reading under which the median matches. The earlier attempt found this claim reproduced under its own criterion (a fraction of units with a one-sided test at p < 0.01, 0.83); the new criterion tests the paper's spikes per touch and latency, and the files' one principal whisker per file lowers the spikes per touch (11 of 20 units in files with several whiskers respond most to another whisker; each unit's best whisker gives a mean of 0.485, a selection biased upward that the criterion does not make).", "deviations": [ "The files give one principal whisker per VPM file, though the session description says each unit has its own; the file's principal whisker is used for every unit." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "vpm-whisking", "statement": "VPM neurons fire at 5.1 +- 5.5 spikes/s without whisker movement or touch; most (25 of 29) increase their rate during whisking without touch, and the mean rate rises from 5.1 to 13.5 spikes/s. Three of 29 do not increase with whisking but still respond to touch.", "source": "Results, Chronic extracellular recordings from somatosensory thalamus, paragraphs 1 and 2; Figure 1c,e; Figure 5d,e; Supplementary Figure 2b,c", "quote": "Typical VPM neurons showed significant spike rates (mean \u00b1 s.d., 5.1 \u00b1 5.5 spikes per s; median, 3.3 spikes per s; n = 29 neurons), even in the absence of whisker movement and touch. ... Most VPM neurons increased their spike rate during whisking in the absence of touch (25 out of 29 neurons ... The average spike rate increased severalfold after onset of whisker movement (from 5.1 \u00b1 5.5 spikes per s to 13.5 \u00b1 12.7 spikes per s; P = 4 \u00d7 10\u22126; n = 29 neurons, Wilcoxon signed-rank test", "statistics": [ { "about": "nonwhisking against whisking spike rate over VPM neurons", "test": "Wilcoxon signed-rank test", "p": 4e-06, "n": "29 neurons" } ], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "The whisking rate exceeds the nonwhisking rate over the 29 units under every filter (O1), sample (O2) and touch reading (O11) (signed-rank p = 5.2e-08 zero-phase and 7.1e-08 forward for the main epochs; higher in 28). Significant increases number 21 to 25 over the 16 readings, outside 25 +- 2.5 under some. Mean nonwhisking rate 3.74 to 3.96 spikes/s and median 1.71 to 1.86, outside tolerance under every reading; mean whisking rate 11.01 to 12.09, within 13.5 +- 2.36 under some readings only. The earlier attempt found this reproduced under its own criterion (a phase-modulation test, 0.88 of units); the new criterion asks for the paper's rates, which are lower here.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "vpm-whisking-phase", "statement": "The spike rate of VPM neurons is modulated by the phase of whisker movement.", "source": "Results, Chronic extracellular recordings from somatosensory thalamus, paragraph 2; Supplementary Figure 2d-f", "quote": "The spike rate was modulated by the phase of the movement (Supplementary Fig. 2d).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "25 to 27 of 29 units have r2 > 0.25 for a sinusoid fit of rate in 12 phase bins under both filters and every O11 reading (25 zero-phase and 27 forward for the main epochs). With spikes moved to the next trial, 16 of 29 units also pass, so the r2 threshold marks more than half of the units on a null; the criterion does not ask for a null, and the units' own spikes give a higher r2 (p = 0.0015). New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-vm-touch-whisking", "statement": "In L4 excitatory neurons (37 whole-cell), resting Vm spans -76 to -45 mV (-63 +- 8 mV); every neuron depolarizes after touch (latency 4.8 +- 0.8 ms, amplitude 6.0 +- 2.9 mV), while whisking causes only a small depolarization or hyperpolarization (1.2 +- 2.1 mV).", "source": "Results, Membrane-potential dynamics of L4 excitatory neurons, paragraph 2; Figure 2f", "quote": "Across the excitatory population, the resting membrane potential (Vm) spanned a large range (\u221276 to \u221245 mV, mean \u00b1 s.d., \u221263 \u00b1 8 mV; median, \u221264 mV, n = 37 neurons ... Touches evoked short-latency depolarizations (latency: mean \u00b1 s.d., 4.8 \u00b1 0.8 ms; median, 4.7 ms; amplitude: mean \u00b1 s.d., 6.0 \u00b1 2.9 mV; median, 5.7 mV; n = 37 neurons) for all neurons (Fig. 2f) ... Whisking induced small depolarization or hyperpolarization (mean \u00b1 s.d., 1.2 \u00b1 2.1 mV; median, 1.2 mV; Fig. 2f)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "51 whole-cell excitatory cells (the paper has 37 control cells); 48 have at least 5 touches, and all 48 have a positive touch PSP and a latency. Resting Vm mean -61.69 mV (O4 a; -61.89 O4 b) is within tolerance under every reading. The touch amplitude (4.78 mV) and the latency (7.68 ms with dVm/dt at the sampling rate, median 4.90) are outside tolerance and do not depend on the whisking readings. A diagnostic shows that the latency rule picks single-sample excursions of dVm/dt in 5 cells (under 1 ms) and late crossings in others (up to 101 ms); subtracting the baseline's mean dVm/dt, which decides nothing, gives 7.48 ms. Under the 16 combinations of O10, O11 and the two filters, the whisking change with the onset windows (reading a) ranges from 0.65 to 0.87 mV and is within 1.2 +- 0.35 in 2 (zero-phase, O10 a, O11 b-i 0.87 mV and b-ii 0.86 mV); the measured value, 0.83 mV, is the first reading the criterion lists (zero-phase, O10 a, O11 a-i), outside tolerance, and with the epochs (reading b) it is 1.08 to 1.14 mV, within tolerance in all 16. Without the 8 cells of the flagged mice the amplitude is 5.54 mV and the latency 4.97 ms, both within; that variant does not decide. Amplitudes go down to 0.01 mV, so that every neuron depolarizes is a weak test. Trials of the PV-ChR2 cell held near 0 mV are left out, and its resting Vm is -38.8 mV. The 26 VGAT-ChR2 cells with too few pulses to tag count as excitatory and include a whole-cell cell with 11,087 spikes 0.37 ms wide, likely FS, so the group probably holds some FS cells. New claim.", "deviations": [ "The group includes the whole-cell cells of ION-cut mice, which the files do not mark, and 4 more PV-IRES-Cre whole-cell cells than Supplementary Table 2 counts.", "Under O11 the 250 ms touch-free rule of whisking onsets uses the touches of the whiskers the reading names; the main rule (every tracked whisker bounding the epochs, principal-whisker touches in the 250 ms rule) is shown beside them.", "Trials whose median Vm is above -20 mV (13 trials of the PV-ChR2 cell, held near 0 mV by current) are left out at rest, a standard choice." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-threshold-touch-vs-whisking", "statement": "Touch moves the membrane potential of L4 excitatory neurons much closer to spike threshold than whisking does (shift 6.1 +- 3.2 mV against 1.1 +- 2.0 mV).", "source": "Results, Membrane-potential dynamics of L4 excitatory neurons, paragraph 2; Figure 2g,h", "quote": "Compared to whisking, touch caused a larger shift of membrane potential toward spike threshold (whisking, 1.1 \u00b1 2.0 mV; touch, 6.1 \u00b1 3.2 mV; P = 1 \u00d7 10\u22127, Wilcoxon signed-rank test; Fig. 2g,h)", "statistics": [ { "about": "touch against whisking shift toward threshold", "test": "Wilcoxon signed-rank test", "p": 1e-07, "n": "37 neurons" } ], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "Over 50 whole-cell excitatory cells the touch shift exceeds the whisking shift in 43 or 44 under every filter and O11 reading (signed-rank p = 9e-11 to 1.3e-10). Means, whisking 0.84 to 1.16 mV (within 1.1 +- 0.33 under every reading), touch 4.60 to 4.67 mV (outside 6.1 +- 0.61). The two threshold readings O3 give the same values (a cell's median threshold differs by at most 0.0089 mV and 8 of 41,620 spikes change threshold). 17 cells have no spikes and take the default threshold of -42 mV. With the held trials of the PV-ChR2 cell left out, the main whisking shift is 0.84 mV, within tolerance, and the touch shift 4.62 mV, outside. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-effective-reversal", "statement": "The effective reversal potential of the touch response of L4 excitatory neurons is more depolarized than resting Vm, while that of whisking is close to rest and more hyperpolarized than that of touch.", "source": "Results, Membrane-potential dynamics of L4 excitatory neurons, paragraph 2; Supplementary Figure 4", "quote": "of the touch response was more depolarized than the resting Vm and sometimes crossed the spike threshold ... In contrast, the effective reversal potential for whisker movement was close to the resting Vm, below the spike threshold and more hyperpolarized than that for touch", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "Per neuron (47 or 48 with both fits) the touch reversal (median -50.0 mV, the mean of the middle two, -50.23 and -49.77 mV) lies above the whisking reversal (median -57.4 to -60.9 mV over the filters and the O10 and O11 readings) in 38 to 40 neurons and above the median resting Vm (-63.9 mV). Pooled fits give -31.90 mV for touch and -51.6 to -56.3 mV for whisking. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-inhibition-timing", "statement": "With L4 excitatory neurons depolarized near 0 mV to reveal inhibition, touch evokes strong, transient inhibition that follows excitation by 0.4 +- 0.8 ms at half maximum.", "source": "Results, Membrane-potential dynamics of L4 excitatory neurons, paragraph 3; Figure 3b-d", "quote": "Touch elicited strong and transient inhibitory input (Fig. 3b,c), which followed excitation with a short delay (mean \u00b1 s.d., 0.4 \u00b1 0.8 ms at half max; n = 6 neurons; Fig. 3d).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Only one whole-cell file has trials held near 0 mV (13 trials of the PV-ChR2 cell, which Supplementary Table 2 counts as FS). No other file pairs a whole-cell trace with a depolarizing current: the 17 cell-attached files of VGAT-ChR2 mice that carry a stored current of about 1.9 in every trial have traces near 0 mV with a 1 to 100 Hz s.d. of at most 0.33 mV (whole-cell median 1.95 mV), and only one cell-attached file has a trial-median trace below -20 mV. The 6 excitatory neurons recorded at rest and with steady depolarizing current are not in the dandiset. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-inhibition-whisking", "statement": "In L4 excitatory neurons held near 0 mV, inhibitory inputs occur spontaneously but are more prevalent at the onset of whisker movement; after whisking onset, excitation and inhibition increase gradually, with indistinguishable time courses, over about 100 ms.", "source": "Results, Membrane-potential dynamics of L4 excitatory neurons, paragraph 3; Figure 3e-g", "quote": "In the absence of touch, inhibitory inputs occurred spontaneously but were more prevalent at onset of whisker movement (Fig. 3e,f). ... After the onset of whisker movement, excitation and inhibition increased gradually, with indistinguishable time courses, over approximately 100 ms (Fig. 3g).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Depends on exc-inhibition-timing; the same 6 depolarized recordings are missing. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fs-touch-response", "statement": "L4 FS interneurons fire at 9.3 +- 8.5 spikes/s without whisker movement and fire 1.9 +- 1.0 spikes per touch, with a spike latency of 5.3 +- 2.1 ms.", "source": "Results, Dynamics of L4 fast-spiking interneurons, paragraph 1; Figure 5b,c", "quote": "FS interneurons were active during baseline conditions, even in the absence of whisker movements (mean \u00b1 s.d., 9.3 \u00b1 8.5 spikes per s; median, 6.4 spikes per s; n = 26 neurons ... and spike rates increased after touch (mean \u00b1 s.d., 1.9 \u00b1 1.0 spikes per touch; median, 1.9 spikes per touch; n = 26 neurons ... and spiking (mean \u00b1 s.d., 5.3 \u00b1 2.1 ms; median, 4.5 ms, n = 24 neurons; Fig. 5c)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_yu_2016.ipynb", "notes": "The four FS readings of the criterion give different outcomes. Under (a)(i), driven at p < 0.001 and inside the boundary, 17 FS cells have a principal whisker (paper 26); the nonwhisking rate 8.53 spikes/s (8.52 to 8.72 over the O11 readings and filters) and the latency 5.23 ms (bin edge, O9 a) or 5.73 ms (centre, O9 b) over 13 cells are within tolerance, and spikes per touch 1.50 is outside 1.9 +- 0.2, so two of three values match (partially reproduced); (b)(i) gives the same cells. Without the boundary, (a)(ii) has 25 cells (8.73 spikes/s, 1.48 spikes per touch, latency 6.16 or 6.66 ms) and (b)(ii) 28 (8.71, 1.39, 10.64 or 11.14 ms), with only the nonwhisking rate within tolerance (not reproduced). The counts against Supplementary Table 2 are 4 VGAT-ChR2 whole-cell FS cells under every reading (paper 5) and 12, 20, 12 and 23 cell-attached ones under (a)(i), (a)(ii), (b)(i) and (b)(ii) (paper 24, 14 control and 10 ION-cut), so the readings without the boundary come closer to the paper's count. The tag test now counts every pulse of the 5 and 10 Hz trains; it drives the same 24 VGAT-ChR2 cells as the earlier rule of isolated pulses. Changed after verification round 1 from partially reproduced, as the criterion's rule for readings that disagree requires. New claim.", "deviations": [ "The light-driven test (one-sided binomial test of a spike 0 to 5 ms after each pulse of the 5 and 10 Hz trains, previous pulse more than 60 ms earlier, against the same 5 ms 50 ms earlier) and the waveform measures (peak-to-trough time and peak to trough ratio of the 300 Hz high-passed mean spike, larger deflection made positive) are this attempt's, as the paper gives neither; every FS group includes FS cells of ION-cut mice, which the files do not mark.", "26 VGAT-ChR2 cells have fewer than 10 short pulses at any cortical site, so no tag test can be run, and they count as excitatory." ], "disagreed": true, "data": "dataset", "where": null, "proposed": null }, { "claim": "fs-vm-touch-whisking", "statement": "In whole-cell L4 FS interneurons (n = 7), touch depolarizes the membrane by 7.0 +- 5.2 mV with onset 4.0 +- 0.6 ms, and whisking depolarizes it by 2.7 +- 2.1 mV toward threshold.", "source": "Results, Dynamics of L4 fast-spiking interneurons, paragraphs 1 and 2; Figure 4d-h", "quote": "Membrane potential depolarized (mean \u00b1 s.d., 7.0 \u00b1 5.2 mV; median, 6.7 mV; n = 7 neurons, Fig. 4d,f) ... Response latencies were short for membrane potential depolarization (onset ... 4.0 \u00b1 0.6 ms; median, 4.2 ms, n = 7 neurons; Fig. 4d,f) ... after onset of whisking, the membrane potential of FS neurons depolarized closer to spike threshold (mean \u00b1 s.d., 2.7 \u00b1 2.1 mV; median, 2.4 mV, n = 7 neurons; Fig. 4e\u2013h)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "5 whole-cell FS cells (paper 7). Touch amplitude 5.56 mV and whisking depolarization 2.54 mV (onset windows; 2.24 forward filter; 1.47 to 2.55 over the O10 and O11 readings, within tolerance in 12 of 16) are within tolerance; the threshold-distance reading gives 1.01 mV, outside. The touch latency with dVm/dt at the sampling rate averages 1.88 ms (median 1.35), outside 4.0 +- 0.4. In the two cells at 0.00 and 0.30 ms the first crossing is a single sample of dVm/dt just above the threshold (0.96 against 0.71 and 3.05 against 1.85 mV/ms), in averages whose Vm lies 0.26 to 0.46 mV above the pre-touch mean at onset; subtracting the baseline's mean dVm/dt, which decides nothing, gives 1.76 ms. So the touch values are not all within tolerance. New claim.", "deviations": [ "The PV-ChR2 cell, FS in Supplementary Table 2, has spikes 0.44 ms wide here and falls outside the 0.35 ms rule for lines without a tag; adding it is shown as a variant." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fs-whisking-rate", "statement": "Most L4 FS interneurons (23 of 26) increase their spike rate during whisking without touch and 3 of 26 decrease it; over the population the rate roughly doubles (to 21.1 +- 15.8 spikes/s).", "source": "Results, Dynamics of L4 fast-spiking interneurons, paragraph 2; Figure 5d,e", "quote": "most L4 FS neurons significantly increased their spike rate during whisker movement without touch (23 of 26 neurons ... and a small subset (3 of 26 neurons ... decreased spike rate. Overall, after onset of whisking ... and the spike rate doubled (mean \u00b1 s.d., 21.1 \u00b1 15.8 spikes per s; median, 14.6 spikes per s, n = 26 neurons, P = 2.7 \u00d7 10\u22125; Fig. 5d)", "statistics": [ { "about": "nonwhisking against whisking spike rate over FS neurons", "p": 2.7e-05, "n": "26 neurons" } ], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "Over 17 FS cells the whisking rate exceeds the nonwhisking rate under every filter, sample and O11 reading (signed-rank p = 0.0002 to 0.0005). 13 or 14 cells increase and 1 to 3 decrease (rank-sum p < 0.05), so the increase count is outside 23 +- 2.3 under every reading. Mean whisking rate 19.02 to 19.17 spikes/s with the zero-phase filter (within 21.1 +- 3.1) and 17.77 to 17.91 with the forward filter (outside). New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fs-whisking-phase", "statement": "Spikes of L4 FS interneurons are coupled to whisking phase.", "source": "Results, Dynamics of L4 fast-spiking interneurons, paragraph 2; Supplementary Figure 7d,g", "quote": "Spikes of L4 FS neurons were also coupled to whisking phase (Supplementary Fig. 7).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "15 or 16 of 17 FS cells have r2 > 0.25 under both filters and every O11 reading (16 for the main epochs; 5 and 3 with the double fit). With spikes moved to the next trial 9 of 17 also pass, which the criterion does not ask for. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fs-touch-and-whisking", "statement": "Touch- and whisking-evoked spikes are typically multiplexed in individual L4 FS neurons, as in VPM neurons.", "source": "Results, Dynamics of L4 fast-spiking interneurons, paragraph 3; Figure 5b,d; Supplementary Figure 7", "quote": "Touch- and whisking-evoked spikes were typically multiplexed in individual L4 FS neurons (Fig. 5b,d and Supplementary Fig. 7), as in VPM neurons.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "11 or 12 of 17 FS cells (0.65 to 0.71) have spikes per touch with a 95% interval above zero and a whisking rate that differs from the nonwhisking rate, under every filter, sample and O11 reading; VPM units give 18 to 22 of 29 (0.62 to 0.76). The earlier attempt also found it reproduced (13 of 20 tagged cells touch-responsive and 16 modulated by phase, by its own measures); the outcome is the same under the paper's measures and the claims file's FS rule.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-mainly-touch", "statement": "L4 excitatory neurons respond mostly to touch (0.3 +- 0.4 spikes per touch, n = 85) and only weakly to whisker movement; their rate does not change significantly between nonwhisking and whisking (0.4 to 0.6 spikes/s, P = 0.20).", "source": "Results, Dynamics of L4 fast-spiking interneurons, paragraph 3; Figure 5b,d,e", "quote": "Excitatory neurons responded mostly to touch (mean \u00b1 s.d., 0.3 \u00b1 0.4 spikes per touch; median, 0.1 spikes per touch; n = 85 neurons; Fig. 5b,d) and showed weak response to whisker movement ... (nonwhisking ... 0.4 \u00b1 0.6 spikes per s; median, 0.1 spikes per s; whisking ... 0.6 \u00b1 0.9 spikes per s; median, 0.2 spikes per s; n = 85, P = 0.20; Fig. 5d,e). In contrast to VPM and L4 FS neurons, L4 excitatory neurons responded selectively to touch", "statistics": [ { "about": "nonwhisking against whisking spike rate over L4 excitatory neurons", "p": 0.2, "n": "85 neurons" } ], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "The 97 excitatory cells fire more during whisking than without it under every filter and O11 reading (signed-rank p = 9.1e-07 zero-phase and 8.7e-06 forward for the main epochs, at most 8.7e-06 over all; higher in 50 to 58), so the paper's test finds a difference where the paper found none (P = 0.20). Spikes per touch 0.320 is within tolerance; the nonwhisking (1.53 to 1.59) and whisking (3.38 to 3.64 spikes/s) rates are above 0.4 and 0.6. Cell-attached cells fire more than whole-cell ones (2.45 against 0.70 spikes/s without whisking), and the whole-cell cells, whose detection is clean, still fire above the paper's 0.4 spikes/s. The cell-attached detection has 5.0% of interspike intervals under 1.5 ms in the median cell, but a 2 ms dead time removes only 8.1% of the cell-attached E spikes (mean rate 6.20 to 5.70 spikes/s over all time), so double detection does not explain the high rates. The earlier attempt also found it not reproduced, under a touch-selectivity index the paper does not use (one-sided p = 0.074 and 0.090); the same outcome now comes from the paper's own test of whisking against nonwhisking rate.", "deviations": [ "The group holds 97 cells against 85, with the excitatory cells of ION-cut mice and 26 VGAT-ChR2 cells that have too few cortical pulses to be tagged; FS cells that the rules cannot find (the fourth PV cell, and 5 of the 29 VGAT-ChR2 FS cells of Supplementary Table 2 that no test here finds driven) may be among them. The 26 untested cells include a whole-cell cell with 11,087 spikes 0.37 ms wide and a cell-attached cell with 16,350 spikes, both likely FS." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "vpm-photoinhibition", "statement": "Photoactivating TRN axons in VPM of VGAT-ChR2-EYFP mice reduces thalamic activity to 17% of control.", "source": "Results, Inhibition is driven by thalamus, paragraph 1; Figure 6b,c", "quote": "Photoactivation of TRN axons reduced activity in the thalamus (to 17% of control, P = 3 \u00d7 10\u22124, n = 17 multiunit recordings; Fig. 6b,c).", "statistics": [ { "p": 0.0003, "n": "17 multiunit recordings" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The 17 thalamic multiunit recordings made by pipette during photoinhibition are not in the dandiset. All 130 single-cell files are in barrel cortex layer 4, and the 18 VPM silicon probe files hold no photostimulation series. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-thalamus-photoinhibition", "statement": "Thalamic photoinhibition hyperpolarizes L4 excitatory neurons and reduces their Vm fluctuations, with an onset latency of 4.2 ms, longer than the 2.8 ms latency of direct cortical GABAergic activation.", "source": "Results, Inhibition is driven by thalamus, paragraph 1; Supplementary Figure 9a-f", "quote": "photoinhibition of thalamus hyperpolarized excitatory neurons and reduced the amplitudes of their membrane voltage fluctuations (Supplementary Fig. 9a\u2013e). Onset latency of Vm hyperpolarization induced by thalamus inactivation was 4.2 ms. This was longer than the 2.8-ms latency measured with direct cortical GABAergic activation (Supplementary Fig. 9f)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "13 whole-cell excitatory cells with thalamic light (paper 12). Vm is lower with light in 12 (median -4.02 mV, signed-rank p = 0.00049) and Vm variance above 10 Hz lower in 10 (median ratio 0.55), under both window readings. With dVm/dt at the sampling rate the onset latency of the grand average is 0.10 ms for both the thalamic light (13 cells) and the cortical tag pulses (14 cells, now that every pulse of a train counts), against 4.2 and 2.8 ms, so neither latency is within tolerance and the thalamic one is not longer. The crossing at 0.1 ms is one sample that drops by 0.061 mV (thalamic) and 0.064 mV (cortical) and returns at the next sample, a transient at light onset; the first crossing 2 ms or more after onset, which decides nothing, is at 4.9 ms (thalamic) and 5.2 ms (cortical), but against different thresholds (-0.0206 and -0.0557 mV per sample; 1 and 3 of 250 baseline samples cross them), so it does not compare the two. The 1 ms bins (5.0 against 3.0 ms) and the 0.5 ms grand averages, which start to fall at about 4.5 to 5 ms (thalamic) and about 3 ms (cortical), put the thalamic onset later, as in the paper; neither is the criterion's rule and neither decides. New claim.", "deviations": [ "The latency rule for laser onset is the touch rule turned downward, an assumption the claims file states. The crossing at 0.1 ms is a one-sample transient at light onset.", "20 kHz averages are brought to 10 kHz by the mean of each pair of samples (standard)." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "thalamus-drives-fs", "statement": "Photoinhibiting the thalamus reduces the spike rates of L4 FS interneurons during nonwhisking (to 4% of control), whisking (to 13%) and touch (to 32%), so FS interneurons are driven by thalamic input.", "source": "Results, Inhibition is driven by thalamus, paragraph 2; Figure 6d,e; Supplementary Figure 9j", "quote": "Photoinhibition reduced spike rates in FS interneurons during nonwhisking (to 4% of control ... and whisking epochs (to 13% of control ... as well as in response to touch (to 32% of control ... FS interneurons were thus driven by input from the thalamus.", "statistics": [ { "about": "nonwhisking spike rate with and without thalamic photoinhibition", "p": 0.0005, "n": "13 neurons" }, { "about": "whisking spike rate with and without thalamic photoinhibition", "p": 6e-05, "n": "15 neurons" }, { "about": "touch response with and without thalamic photoinhibition", "p": 0.0001, "n": "14 neurons" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": "reproduce_yu_2016.ipynb", "notes": "Too few cells under the claim's own rule. Only 5 FS cells by the claims file's rule were recorded with thalamic light, all from anm260070, and a two-sided signed-rank test of 5 cells cannot go below p = 0.0625 (0.062 to 0.12 over every reading). The rates fall with the light in 5 of 5 cells without whisking and 4 of 5 with it, to 0.204 and 0.273 of control and spikes per touch to 0.410 (population means, all powers, control in the same span, main epochs); over the 32 combinations of filter, window, power and O11 reading the fractions are 0 to 0.32 without whisking and 0.15 to 0.29 with it. The one-sided variant gives p = 0.031 for the nonwhisking rate and spikes per touch and 0.062 for the whisking rate, so it would not pass either. Without the waveform boundary (9 cells, a reading of fs-touch-response only) all three two-sided tests pass (p = 0.012, 0.0078 and 0.0039) and the fractions are 0.199, 0.292 and 0.462, outside tolerance, so the best outcome it could give is partially reproduced. The earlier attempt found this reproduced from 9 tagged cells and their overall rate (median ratio 0.40); the new criterion applies the waveform boundary, which leaves 5 cells.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "rabies-vpm-input", "statement": "Monosynaptic rabies tracing from L4 PV interneurons labels thalamic neurons mostly in VPM (>90%) and few in POM (<10%).", "source": "Results, Inhibition is driven by thalamus, paragraph 3; Supplementary Figure 10", "quote": "The vast majority of trans-synaptically labeled thalamic neurons were in VPM (>90%), with only a small minority in POM (<10%; Supplementary Fig. 10).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds no histology or image data; the rabies tracing sections are not in it. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "ion-cut-exc-no-touch", "statement": "After infraorbital nerve transection, L4 excitatory neurons do not depolarize after touch.", "source": "Results, Inhibition is driven by sensory input, paragraph 2; Figure 7b", "quote": "As expected, L4 excitatory neurons did not depolarize after touch (Fig. 7b).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No file marks the ION-cut mice. 4 VGAT-ChR2 mice flagged here (no touch input or performance below 0.5) hold 8 whole-cell excitatory cells whose touch PSPs average 0.35 mV against 5.54 mV in the others, but they were found by that property, so they cannot test the claim. Supplementary Table 2 suggests the ION-cut mice had no fibre in VPM; the 4 flagged mice are among the 15 VGAT-ChR2 mice without a VPM light site (none of the 12 with one is flagged). Of the other 11, 8 have touch PSPs of 3.85 to 10.84 mV; the remaining 3 (anm281589, anm281592, anm318531) have no touch PSP of 1 mV or more, but each has a cell whose spikes per touch has a 95% interval above zero, so they are weak candidates at most. That gives at most 7 candidates for 9 ION-cut mice, so the files cannot confirm the cut mice. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "ion-cut-exc-whisking", "statement": "After ION transection, whisking-evoked depolarization of L4 excitatory neurons is reduced (0.62 +- 0.50 mV, n = 9) relative to control neurons with matched resting potential (1.54 +- 0.79 mV, n = 15).", "source": "Results, Inhibition is driven by sensory input, paragraph 2; Figure 7c,d", "quote": "Depolarizations in response to whisker movement were reduced (ION cut: mean \u00b1 s.d., 0.62 \u00b1 0.50 mV, n = 9 neurons versus Control with matched resting potential: mean \u00b1 s.d., 1.54 \u00b1 0.79 mV, n = 15 neurons; P = 0.005, Wilcoxon rank-sum test; Fig. 7c,d)", "statistics": [ { "test": "Wilcoxon rank-sum test", "p": 0.005, "n": "9 ION-cut and 15 control neurons" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As for ion-cut-exc-no-touch. The flagged mice's whole-cell cells have a whisking change of 0.39 mV on average (epochs reading), shown as not a test. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "ion-cut-exc-phase", "statement": "After ION transection, phase-locking of L4 excitatory Vm to whisker movement is abolished (coupling 0.12 +- 0.04 mV against 0.38 +- 0.31 mV in controls).", "source": "Results, Inhibition is driven by sensory input, paragraph 2; Figure 7e", "quote": "phase-locking of membrane potential to whisker movement was abolished (ION cut, 0.12 \u00b1 0.04 mV versus Control, 0.38 \u00b1 0.31 mV; P = 0.005; Fig. 7e)", "statistics": [ { "p": 0.005, "n": "9 ION-cut and 15 control neurons (the n of the same sentence)" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As for ion-cut-exc-no-touch. The flagged mice's Vm phase coupling averages 0.11 mV, shown as not a test. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "ion-cut-fs-no-touch", "statement": "After ION transection, touch does not evoke spikes in L4 FS interneurons.", "source": "Results, Inhibition is driven by sensory input, paragraph 3; Figure 7g", "quote": "Touch did not evoke spikes in FS interneurons (Fig. 7g).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No file marks the ION-cut mice. The 2 FS cells (by the claims file's rule) of the flagged mice average 0.09 spikes per touch, shown as not a test. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "sensory-input-drives-fs", "statement": "After ION transection, the whisking-related activation of L4 FS interneurons is absent in most cells (P = 0.80, n = 10), so their movement-related modulation is reafference driven by sensory input.", "source": "Results, Inhibition is driven by sensory input, paragraph 3; Figure 7h,i", "quote": "In addition, whisking-related activation of FS interneurons was also absent in most cells (P = 0.80, n = 10 neurons; Fig. 7h,i). ... These data show that excitation of L4 excitatory neurons and L4 FS neurons is dominated by sensory input. Modulation correlated with whisker movement in L4 FS neurons constitutes reafference.", "statistics": [ { "about": "nonwhisking against whisking spike rate of FS cells after ION cut", "p": 0.8, "n": "10 neurons" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No file marks the ION-cut mice (no ION, nerve, transection, lesion, cut, surgery or sham in any metadata text). The 2 FS cells of the flagged mice fire 8.37 spikes/s without whisking and 9.98 with it, shown as not a test. The earlier attempt was blocked for the same reason; the outcome is unchanged.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "ion-cut-fs-phase", "statement": "After ION transection, phase-locking of L4 FS spikes to whisker movement is reduced but not entirely abolished.", "source": "Results, Inhibition is driven by sensory input, paragraph 3; Supplementary Figure 12", "quote": "Phase-locking of spikes to whisker movement was reduced but not entirely abolished (Supplementary Fig. 12).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As for sensory-input-drives-fs. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "ion-cut-behavior", "statement": "After infraorbital nerve transection, mice still search for the pole by whisking but, unable to sense it, perform the task at chance (48% correct).", "source": "Results, Inhibition is driven by sensory input, paragraph 2", "quote": "however, as they were unable to sense the object, ... they performed at chance level (48% correct).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The ION-cut sessions cannot be identified. Two of the flagged mice were flagged by performance below 0.5, so their performance cannot test the claim. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "pv-enphr-suppression", "statement": "Yellow light in PV-IRES-Cre mice expressing eNpHR3.0 strongly inhibits most L4 PV interneurons (3 of 4); their rate falls 3 ms after laser onset and L4 excitatory activity rises 2 ms later.", "source": "Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 7; Supplementary Figure 13a,c", "quote": "First, the spike rate of L4 PV interneurons decreased 3 ms after laser onset, and activity in L4 neurons increased only 2 ms later (Supplementary Fig. 13c) ... Four L4 PV interneurons recorded. 3 out of 4 are strongly inhibited by eNpHR stimulation.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "3 PV cells are identified by their inactivation (the paper has 4), and all 3 are strongly inhibited (light rate below the lower bound of the control 95% interval in nonwhisking and whisking periods). The count cannot fail, since the cells are found by their inactivation, and a fourth PV cell that the light did not inhibit would be classed excitatory. The parts that can fail fail: in the grand average PSTH aligned to laser onset the dPSTH/dt rule finds no fall for the 3 PV cells and a rise at 48.0 ms (bin edge, O9 a) or 48.5 ms (centre, O9 b) for the 42 excitatory cells, so neither latency is within tolerance under either bin position. New claim.", "deviations": [ "The latency rule for laser onset is the Methods' spike-latency rule, an assumption the claims file states. The PV grand average rises in the first 3 ms after onset (66.5 spikes/s at 1 ms) before falling to 0, possibly an onset artifact." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fs-suppress-movement-spiking", "statement": "Partially suppressing PV (FS) interneurons increases the spike rate of L4 excitatory neurons during nonwhisking (0.6 to 1.6 spikes/s) and whisking (0.8 to 2.7 spikes/s).", "source": "Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 1; Figure 8b-d; Supplementary Figure 13b", "quote": "Partially suppressing PV (FS) interneurons changed the responses of excitatory neurons (Fig. 8b\u2013e; P = 1 \u00d7 10\u22126, Kruskal-Wallis test). L4 excitatory neurons increased their spike rate during both nonwhisking periods (from 0.6 \u00b1 0.1 spikes per s to 1.6 \u00b1 0.3 spikes per s; mean \u00b1 s.e.m., n = 40 neurons, P = 6 \u00d7 10\u22125) and whisking periods(from 0.8 \u00b1 0.2 spikes per s to 2.7 \u00b1 0.5 spikes per s, P = 2 \u00d7 10\u22126", "statistics": [ { "about": "rates of excitatory neurons across conditions", "test": "Kruskal-Wallis test", "p": 1e-06, "n": "40 neurons" }, { "about": "nonwhisking rate, control against eNpHR", "p": 6e-05, "n": "40 neurons" }, { "about": "whisking rate, control against eNpHR", "p": 2e-06, "n": "40 neurons" } ], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "In the 42 excitatory cells of PV-IRES-Cre mice (paper 40) the light raises the nonwhisking rate (32 to 36 cells, p at most 7.4e-05) and the whisking rate (31 to 34 cells, p at most 0.0003) under every filter, window and O11 reading (Kruskal-Wallis p = 2.7e-05 to 0.00035, reported only). The rates are higher than the paper's (control 1.18 to 1.32 rising to 2.26 to 2.55 spikes/s without whisking, 3.36 to 4.31 rising to 5.69 to 6.63 with it, against 0.6 to 1.6 and 0.8 to 2.7), outside tolerance; 34 of the 42 cells are cell-attached, whose rates are high throughout the dandiset. The measured values are zero-phase, control in the light span, main epochs. The earlier attempt found this reproduced from 7 whole-cell cells inside the light (6 of 7 rising, p = 0.016); the new criterion uses all excitatory cells and also tests the paper's rates, which are not matched.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fs-enhance-touch-selectivity", "statement": "With PV interneurons suppressed, L4 excitatory neurons become driven by whisker movement (whisking rate above nonwhisking, P = 0.02), while in control trials they are not (P = 0.55); their selectivity for touch is normally maintained in part by FS interneurons.", "source": "Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 1; Figure 8d", "quote": "L4 excitatory neurons were instead driven by whisker movements (P = 0.02, Fig. 8d), implying that their selectivity for touch was normally maintained in part by FS interneurons.", "statistics": [ { "about": "nonwhisking against whisking rate in eNpHR trials (Fig. 8d)", "p": 0.02, "n": "40 neurons" }, { "about": "nonwhisking against whisking rate in control trials (Fig. 8d, printed in the figure)", "p": 0.55, "n": "40 neurons" } ], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "With the light, whisking rates exceed nonwhisking rates (31 to 33 of 42 cells, p = 1.7e-06 to 3.7e-05 over the filter, window and O11 readings), as the paper reports (P = 0.02), but in control trials they do too (27 to 35 of 42, p = 6.7e-06 to 0.00013), where the paper found none (P = 0.55). The earlier attempt found it not reproduced by a touch-selectivity index the paper does not use; the new criterion is the paper's test of whisking against nonwhisking rate, whose first part holds.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "exc-touch-spikes-enphr", "statement": "PV interneuron suppression does not change mean touch-evoked spiking of L4 excitatory neurons significantly (0.27 to 0.32 spikes per touch, P = 0.09); its effect is heterogeneous, with weakly responding neurons responding more and strongly responding neurons unchanged or less.", "source": "Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 2; Figure 8e; Supplementary Figure 13b", "quote": "PV interneuron suppression also modulated touch-evoked spiking in L4 excitatory neurons, but they did so in a heterogeneous manner (mean \u00b1 s.e.m., from 0.27 \u00b1 0.06 spikes per touch to 0.32 \u00b1 0.06 spikes per touch, n = 40 neurons, P = 0.09, Wilcoxon signed-rank test; Fig. 8e and Supplementary Fig. 13). Neurons that responded weakly to touch tended to respond more strongly with PV interneuron suppression.", "statistics": [ { "test": "Wilcoxon signed-rank test", "p": 0.09, "n": "40 neurons" } ], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "Spikes per touch (4 to 20 ms after minus 0 to 16 ms before, ITI of at least 10 ms) rise with the light from 0.339 to 0.448 (40 cells, signed-rank p = 0.044, control in the light span) or from 0.304 to 0.442 (41 cells, p = 0.0091, control anywhere), so the test finds a change. Cells below the median control response rise by 0.123 on average, cells above it by 0.095. New claim.", "deviations": [], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "auc-weak-strong", "statement": "Suppressing PV interneurons improves touch detection (AUC) for L4 excitatory neurons with weak touch responses and diminishes it for neurons with robust touch responses.", "source": "Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 3; Figure 8f,g", "quote": "Consistent with the heterogeneous changes in spikes per touch, suppression of PV interneurons improved AUC for neurons with weak responses to touch and diminished AUC for neurons with robust responses to touch (Fig. 8f,g).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "With the fixed seeds (29 and 31), cells whose AUC rises with the light have a lower control touch-evoked rate than cells whose AUC falls, 5.93 against 10.87 spikes/s (reading a, 23 and 12 cells) and 8.14 against 8.18 (reading b, 17 and 16). Over 20 further seeds, reading (a) holds in 19 and reading (b) in 8 (rising group 8.14 to 8.53 against falling group 7.86 to 8.18 spikes/s), so under (b) the sign of a 0.04 spikes/s difference is set by the resampling and the reading does not match; the criterion needs both readings. No rank-sum test separates the groups with the fixed seeds (p = 0.37 and 1, reported only). Changed after verification round 1 from reproduced, on the seed check the verifier asked for. New claim.", "deviations": [ "Where an outcome depends on the random seed, a reading counts as matching only when it matches under most of 20 seeds, a rule of this attempt." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "auc-groups", "statement": "Neurons whose AUC rose with PV suppression gained touch-evoked spiking (3.4 to 8.7 spikes/s); neurons whose AUC fell kept their touch-evoked response (7.3 to 7.0 spikes/s) but had higher baseline rates (0.9 to 2.6 spikes/s).", "source": "Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 4; Figure 8h", "quote": "L4 excitatory neurons with increased AUCs showed a population increase in touch-evoked responses on average (from 3.4 \u00b1 0.8 spikes per s to 8.7 \u00b1 1.9 spikes per s, P = 0.0001). Neurons with reduced AUC showed unchanged touchevoked responses as a population (from 7.3 \u00b1 1.5 spikes per s to 7.0 \u00b1 1.4 spikes per s, P = 0.98, average 0\u2013250 ms after touch onset) ... but elevated baseline spike rates (from 0.9 \u00b1 0.2 spikes per s to 2.6 \u00b1 0.6 spikes per s, mean \u00b1 s.e.m., P = 0.0002; Fig. 8f\u2013h).", "statistics": [ { "about": "touch-evoked rate, control against eNpHR, neurons with increased AUC", "p": 0.0001, "n": "19 neurons (Fig. 8h)" }, { "about": "touch-evoked rate, control against eNpHR, neurons with reduced AUC", "p": 0.98, "n": "21 neurons (Fig. 8h)" }, { "about": "baseline rate, control against eNpHR, neurons with reduced AUC", "p": 0.0002, "n": "21 neurons (Fig. 8h)" } ], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "With the fixed seeds the readings differ. Under (a) the increased-AUC group's response rises (9.99 to 15.16 spikes/s, p = 4.9e-05), the reduced-AUC group's does not change (15.98 to 17.85, p = 0.11) and its baseline rises (5.11 to 12.08, p = 0.0049), with group sizes 23 and 12 and rates outside tolerance; under (b) the reduced-AUC group's response changes (12.37 to 14.95, p = 0.021). Over 20 further seeds the three tests hold in 9 seeds under (a) and in none under (b), where the reduced-AUC group's response changes in every seed (p = 0.015 to 0.045), so neither reading matches under most seeds and the claim is not reproduced. Group sizes range from 15 to 22 (increased) and 11 to 19 (reduced) over seeds. Changed after verification round 1 from blocked (methods underspecified), on the seed check. New claim.", "deviations": [ "Where an outcome depends on the random seed, a reading counts as matching only when it matches under most of 20 seeds, a rule of this attempt." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "behavior-false-alarms", "statement": "With PV interneurons suppressed, most mice (6 of 8) are more likely to report touch with the pole out of reach (false alarms on no-lick trials).", "source": "Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 6; Supplementary Figure 14b,c", "quote": "with PV interneuron suppressed, most mice (6 of 8) were more likely to report touches with the pole out of reach (Supplementary Fig. 14). ... In 8 mice tested, 6 showed a significant decrease of performance during Nolick trials with PV interneuron inactivation", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_yu_2016.ipynb", "notes": "Of 9 PV-IRES-Cre mice with the light (the paper tested 8), 6 show a significant decrease of no-lick performance under reading (b)(i), per session (a mouse counting when any session is significant) and without the continuity correction, which meets 6 of 8. The other readings give 5 ((a)(i), trials pooled, no correction), 4 ((a)(ii), pooled, Yates) and 5 ((b)(ii), per session, Yates); pooled, no mouse shows a significant increase under either test. Mice have 1 to 11 sessions, so reading (b) gives more chances to a mouse with many sessions, and one session of anm244024 shows a significant rise (p = 0.042) while another shows a fall. What the answer changed. The answer of 2026-10-20 says the paper does not state a continuity correction, and the criterion now runs the test without it (what Matlab's crosstab returns) and with Yates's correction. The claim had been blocked as methods underspecified because the two disagreed; under the updated criterion the reading without the correction matches, so it is reproduced. New claim.", "deviations": [ "The dandiset holds 9 PV-IRES-Cre mice with the eNpHR light where the paper tested 8; which mouse the paper left out is not stated, and all 9 are counted." ], "disagreed": false, "data": "dataset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "Still present from 000005-yu-2016-01. No L4 file names the cell type of its neuron; the cell types the paper compares can only be inferred from light tagging, waveforms and light inactivation." }, { "kind": "metadata_insufficient", "statement": "Still present from 000005-yu-2016-01. No file marks the 9 ION-transected mice, and the files hold no surgery or notes field; the ION-cut claims cannot be tested and their cells sit in every control group." }, { "kind": "metadata_error", "statement": "Still present from 000005-yu-2016-01. The genotype is missing for the 6 VPM mice and 3 L4 mice (anm260074, anm223517, anm250509), and the 5 SOM-IRES-Cre x Ai32 mice are given as Ai32." }, { "kind": "metadata_insufficient", "statement": "Still present from 000005-yu-2016-01. Every L4 file gives cortical layer 4 (depth 0.42 to 0.62 mm), so the layer of each cell cannot be checked." }, { "kind": "metadata_insufficient", "statement": "Still present from 000005-yu-2016-01. The optogenetic conditions are not described. photo_stim_mode and type have empty descriptions and the mode labels do not map to one kind of light, photo_stim_power is NaN in every L4 file, and no file names the opsin (eNpHR3.0 in the PV-IRES-Cre mice)." }, { "kind": "metadata_error", "statement": "Still present from 000005-yu-2016-01. The session description gives the wrong recording mode for 24 of 130 L4 files, all from PV-IRES-Cre mice; by the trace PV-IRES-Cre has 9 whole-cell and 39 cell-attached cells where Supplementary Table 2 has 5 and 42." }, { "kind": "metadata_error", "statement": "Still present from 000005-yu-2016-01. In the L4 files the trial table's first_touch_time is the trial start plus the first-touch latency divided by 1000 (it matches the touch series in 0.956 of trials once multiplied by 1000); in the VPM files it is correct." }, { "kind": "metadata_insufficient", "statement": "Still present from 000005-yu-2016-01. The L4 trace is sampled at 10 kHz (92 files) or 20 kHz (38 files), which only the timestamps state." }, { "kind": "metadata_insufficient", "statement": "Still present from 000005-yu-2016-01. 8 files name no principal whisker, and the VPM files give one principal whisker per file though the session description says each unit has its own; 11 of 20 units in files with several tracked whiskers respond most to another whisker." }, { "kind": "other", "statement": "Still present from 000005-yu-2016-01. In VGAT-ChR2 mice the light at the site labelled VPM is given as 594 nm, and isolated pulses at the site labelled vS1 (594 nm) drive 13 VGAT-ChR2 cells at 1.6 to 4.6 ms; ChR2 needs blue light, so the wavelengths look wrong." }, { "kind": "methods_unavailable", "statement": "Still present from 000005-yu-2016-01. Neither the paper nor the dandiset links analysis code. This attempt read the full text, supplied to it, which gives the windows and rules the earlier attempt lacked; the claims file found no code at CRCNS ssc-7." }, { "kind": "metadata_error", "statement": "New. The injected current (CurrentClampStimulus) has unit amperes and conversion 1e-6, but the end-of-trial test pulse, -0.1 nA in the Methods, is stored as about -0.1 (in 14 of 57 whole-cell files), so the stored values are in nA and the conversion is wrong by a factor of 1,000. 17 cell-attached files of VGAT-ChR2 mice carry a constant stored current of about 1.9 in every trial, which no description explains." }, { "kind": "data_missing", "statement": "New. The dandiset lacks data the paper reports from these experiments, namely the 6 L4 excitatory neurons recorded with depolarizing current (Fig. 3; only one whole-cell file, of the PV-ChR2 cell, has trials held near 0 mV), the 17 thalamic multiunit recordings during photoinhibition (Fig. 6b,c), and the rabies tracing histology (Supplementary Fig. 10)." }, { "kind": "other", "statement": "New. The pulse trains at the site labelled VPM run at 50 Hz in 12 of 33 files, where the Methods give 100 Hz." }, { "kind": "metadata_insufficient", "statement": "New. The no-lick trial type is spelled Nogo in some files and NoGo in others, and the type and response columns have empty descriptions." } ], "verifications": [ { "date": "2026-10-20", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The handover of the run recorded in this attempt before this revision, the executed notebook with the conclusions and summary removed, the helper module and the claims file; the verifier also read the paper under paper/ and checked the archive metadata for the blocked claims.", "agreed": 32, "of": 33, "disagreements": [ { "claim": "fs-touch-response", "outcome": "blocked", "reason": "The FS readings disagree. With the waveform boundary, 2 of 3 values are within tolerance (partial); without it, 1 of 3 (not reproduced). Spikes per touch is 1.39 to 1.50 in every reading (needs 1.9 +- 0.2). Only 17 FS cells against the paper's 26. The tag rule (isolated pulses, gap 0.1 s both sides) is the author's own and throws away the 10 Hz tagging trains, leaving 29 of 67 VGAT cells untested; ca_waveform drops 8 of 20 light-driven cells, with ratios up to 19 and durations up to 0.9 ms, which suggests the measure does not match the axes of Supplementary Fig. 6. Every control group includes the ION-cut cells; with the flagged mice left out FS spikes per touch moves from 1.50 to 1.69 and reading (a)(ii) from 1 to 3 values within tolerance." } ] }, { "date": "2026-10-20", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the run recorded after the round-1 revision, with its conclusions and summary, the helper module, the claims file, this record and the README; the verifier also read the paper under paper/.", "agreed": 33, "of": 33, "disagreements": [] } ] } ], "entries": [ { "name": "000005-yu-2016", "type": "reproduction", "title": "VPM and layer 4 responses to touch and whisking, and their control by thalamus and FS interneurons (Yu et al. 2016)", "description": "Tests the claims written from the full text of Yu, Gutnisky, Hires and Svoboda (2016) on dandiset 000005, which holds silicon probe recordings in VPM and single-cell recordings in layer 4 of barrel cortex of mice locating a pole with their whiskers. It measures touch responses, whisking rates and phase coupling of VPM units, FS interneurons and excitatory cells, their membrane potential, and the effects of thalamic photoinhibition and of PV interneuron suppression, by the paper's methods as the claims file gives them.", "datasets": [ "dandi:000005" ], "papers": [ "10.1038/nn.4412" ], "derived_from": [], "notebooks": [ { "path": "reproduce_yu_2016.ipynb", "title": "Reproducing Yu et al. (2016) from dandiset 000005", "executed": "notebooks/000005-yu-2016/reproduce_yu_2016.html" } ] } ] }